Replication of the functionality and isolation provided by enzyme active sites is an important goal in the creation of effective models. To provide both of these attributes, we have covalently incorporated flavin mononucleotide (FMN) into a silicate matrix using the sol-gel process. In these sol-gels, the isolation provided by the cybotactic region of the silicate replicates the sequestered nature of an enzyme active site. Specific hydrogen bonding recognition of the flavin within the sol-gel matrix was then established via doping with diacyl diaminopyridine 3. The presence, specificity, and magnitude of this host-guest interaction was established via quenching of the flavin fluorophore by receptor 3.